.. mapmuts documentation master file, created by
   sphinx-quickstart on Sun Feb 24 15:57:39 2013.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

===========================
`mapmuts`_
===========================

This package is obsolete!
------------------------------

**IMPORTANT NOTE:** `mapmuts`_ has been superseded by `dms_tools`_. Unless you need legacy functions of `mapmuts`_, we suggest that you use `dms_tools`_ instead.

Package overview
--------------------

`mapmuts`_ is a `Python`_ package for mapping mutations from deep-sequencing of protein-coding genes. It is specifically designed for the analysis of overlapping Illumina paired-end reads.

`mapmuts`_ source code is available `on GitHub`_.

`mapmuts documentation`_ is available `on GitHub Pages`_.

The `mapmuts`_ package was created by `Jesse Bloom`_.


Using `mapmuts`_
===================
This package can be run using a series of scripts, and does not require you to directly interface with the `Python`_ modules.

Some examples are provided with the package; they can be found in the ``./examples/`` subdirectory of the main `mapmuts`_ package.


Documentation
===============

.. toctree::
   :maxdepth: 2

   installation
   workflow
   scripts
   examples
   pythonapi
   shortcomings
   acknowledgements


Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`

.. include:: weblinks.txt